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annotate wgmlst_create.xml @ 0:a3cc35af3635 draft

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planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
author bvalot
date Thu, 16 Jun 2022 12:32:28 +0000
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a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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1 <tool id="wgmlst_create_wrapper" name="Create cg/wgMLST database" version="2.1.3">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="2.1.3">pymlst</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" />
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8 </stdio>
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9 <version_command>wgMLST -v</version_command>
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10 <command>
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11 wgMLST create --force
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12 #if $concatenate
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13 -c
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14 #end if
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15 #if $remove
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16 -r
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17 #end if
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18 '${database}' '${coregene}' &amp;> '${logfile}'
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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19 </command>
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20 <inputs>
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21 <param name="coregene" type="data" format="fasta"
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22 label="Multiple fasta with GENES sequence" help="Fasta format" />
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23 <param name="concatenate" type="boolean" checked="false"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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24 label="Automatically concatenate GENES with duplicated sequences" />
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25 <param name="remove" type="boolean" checked="false"
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26 label="Automatically remove GENES with duplicated sequences" />
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27 </inputs>
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28 <outputs>
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29 <data name="logfile" format="txt" label="${tool.name} on ${coregene.name}: log" />
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30 <data name="database" format="sqlite" label="cg/wgMLST database on ${coregene.name}" />
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31 </outputs>
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32 <tests>
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33 <test expect_num_outputs="2">
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34 <param name="coregene" ftype="fasta" value="EHSB-021_gene.fasta" />
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35 <param name="remove" value="true" />
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36 <output name="logfile" ftype="txt">
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37 <assert_contents>
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38 <has_text text="Skipped invalid genes: 99" />
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39 <has_text text="Database initialized" />
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40 </assert_contents>
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41 </output>
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42 </test>
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43 </tests>
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44 <help>
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45 **What it does**
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46
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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47 Create a cg/wgMLST DATABASE from a template COREGENE.
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48
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49 Options:
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50 -c, --concatenate Automatically concatenate GENES with duplicated sequences.
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51 -r, --remove Automatically remove GENES with duplicated sequences.
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52
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53 **License and citation**
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54
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55 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
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56 </help>
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57 <citations>
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58 </citations>
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59 </tool>